Porous starch is one of the widely used multifunctional materials in food and pharmaceutical industries. This work was carried out to prepare porous starch by a novel clean-label method of critical melting (CM) and freeze-thawing (FT) treatment. Porous starch prepared by CMFT showed observable grooves and holes on the surface, channels and cavities inside the granule. Repeated FT after CM promoted the formation of porous structures, in which freezing rates showed different effects on the pore-forming properties of starch granules. Compared to the native counterpart, porous starch prepared by CMFT showed significantly increased thermal stability as shown by water solubility, swelling power, DSC, and RVA. CMFT treatment significantly increased water and oil absorption of porous starch from 85 to 75% (native) up to about 160 and 100%, respectively. Moreover, CMFT prepared porous starch showed the appearance of a visible diffraction peak at 20°, indicating a more ordered double-helical structure in starch granules. The synergistic effect of CM combined with FT could be used to prepare porous starch with “clean-label”.